|
| Status |
Public on Jun 25, 2024 |
| Title |
lin28a, 2TG, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
treatment: heat shock
|
| Treatment protocol |
Embryos underwent 1-hour heat treatment at 2 and 3 dpf to induce the expression of QFvpr which is controlled by hsp70l promotor.
|
| Growth protocol |
Zebrafish embryos were placed in zebrafish E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, and 0.33 mM MgSO4) and raised in a 28.5 °C incubator with a light-dark cycle of 14 h light and 10 h dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was then extracted from 4-dpf embryos using TRIzol (15596026, Invitrogen, USA) or RNAiso Plus (91085, Takara Bio, Japan) following the manufacturer's protocols. At least 1 μg total RNA of each sample was used for the construction of sequencing library.
Construction of RNA libraries was done by the sequencing company (Anoroad) following standard procedures.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
lin28a.2TG_1
|
| Data processing |
Trimmomatic version 0.39
Adapter sequences and low-quality reads were removed.
The resulting sequencing reads were aligned to the Danio rerio genome version GRCz11 (danRer11) using STAR version 2.7.10b.
Transcripts were quantified using Salmon v1.10.1 to determine transcript abundance in terms of TPM (Transcripts per Million).
Assembly: GRCz11
Supplementary files format and content: xlsx files include TPM values for merged gene using salmon and each file contains 6 biological replicates from 2Tg and 3Tg embryos
|
| |
|
| Submission date |
May 26, 2024 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Youngnam N Jin |
| E-mail(s) |
ynjin.neo@gmail.com
|
| Phone |
13628627281
|
| Organization name |
Wuhan University
|
| Department |
Medical Research Institute
|
| Street address |
115 Donghu Road, Wuchang District
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430071 |
| Country |
China |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE268371 |
Precise RNA knockdown of smn1,or tardbp and tarbpl by CRISPR-QKD and transcription activation of lin28a and sox9b by CRISPR-Qa in zebrafish |
|
| Relations |
| BioSample |
SAMN41549138 |
| SRA |
SRX24707880 |
